Searched for: author%3A%22Bertels%2C+K.L.M.%22
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Ren, S. (author), Ahmed, N. (author), Bertels, K.L.M. (author), Al-Ars, Z. (author)
In order to improve the accuracy of indel detection, micro-assembly is used in multiple variant callers, such as the GATK HaplotypeCaller to reassemble reads in a specific region of the genome. Assembly is a computationally intensive process that causes runtime bottlenecks. In this paper, we propose a GPU-based de Bruijn graph construction...
conference paper 2018
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Ashraf, I. (author), Khammassi, N. (author), Taouil, M. (author), Bertels, K.L.M. (author)
The growing demand of processing power is being satisfied mainly by an increase in the number of homogeneous and heterogeneous computing cores in a system. Efficient utilization of these architectures demands analysis of memory-access behaviour of applications and perform data-communication aware mapping of applications on these architectures....
journal article 2018
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Fu, X. (author), Rol, M.A. (author), Bultink, C.C. (author), van Someren, J. (author), Khammassi, N. (author), Ashraf, I. (author), Vermeulen, R.F.L. (author), de Sterke, J.C. (author), Vlothuizen, W.J. (author), Schouten, R.N. (author), Almudever, Carmen G. (author), DiCarlo, L. (author), Bertels, K.L.M. (author)
Quantum computers promise to solve certain problems that are intractable for classical computers, such as factoring large numbers and simulating quantum systems. To date, research in quantum computer engineering has focused primarily at opposite ends of the required system stack: devising high-level programming languages and compilers to...
conference paper 2017
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Versluis, R. (author), Poletto, S. (author), Khammassi, N. (author), Tarasinski, B.M. (author), Haider, S.N. (author), Michalak, D.J. (author), Bruno, A. (author), Bertels, K.L.M. (author), DiCarlo, L. (author)
We present a scalable scheme for executing the error-correction cycle of a monolithic surface-code fabric composed of fast-flux-tunable transmon qubits with nearest-neighbor coupling. An eight-qubit unit cell forms the basis for repeating both the quantum hardware and coherent control, enabling spatial multiplexing. This control uses three...
journal article 2017
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Ahmed, N. (author), Bertels, K.L.M. (author), Al-Ars, Z. (author)
DNA read alignment is a major step in genome analysis. However, as DNA reads continue to become longer, new approaches need to be developed to effectively use these longer reads in the alignment process. Modern aligners commonly use a two-step approach for read alignment: 1. seeding, 2. extension. In this paper, we have investigated various...
conference paper 2016
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Houtgast, E.J. (author), Sima, V.M. (author), Marchiori, G. (author), Bertels, K.L.M. (author), Al-Ars, Z. (author)
Next Generation Sequencing techniques have dramatically reduced the cost of sequencing genetic material, resulting in huge amounts of data being sequenced. The processing of this data poses huge challenges, both from a performance perspective, as well as from a power-efficiency perspective. Heterogeneous computing can help on both fronts, by...
conference paper 2016
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Kritchallo, V.V. (author), Vermij, Erik (author), Bertels, K.L.M. (author), Al-Ars, Z. (author)
This paper presents the concept of a fidelity slider, which is a user-defined method that enables trading off accuracy for performance in a parallelized application. The slider is defined in the context of the Canny edge detector, but can be generalized to other image processing algorithms. The slider moderates discontinuity issues introduced by...
conference paper 2016
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Houtgast, E.J. (author), Sima, V.M. (author), Bertels, K.L.M. (author), Al-Ars, Z. (author)
Next Generation Sequencing techniques have resulted in an exponential growth in the generation of genetics data, the amount of which will soon rival, if not overtake, other Big Data elds, such as astronomy and streaming video services.<br/>To become useful, this data requires processing by a complex pipeline of algorithms, taking multiple days...
journal article 2016
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Houtgast, E.J. (author), Sima, V.M. (author), Bertels, K.L.M. (author), Al-Ars, Z. (author)
We are rapidly entering the era of genomics. The dramatic cost reduction of DNA sequencing due to the introduction of Next Generation Sequencing (NGS) techniques has resulted in an exponential growth of genetics data. The amount of data generated, and its associated processing into useful information, poses serious computational challenges. Here...
abstract 2016
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Haron, M.A.B. (author), Yu, J. (author), Nane, R. (author), Taouil, M. (author), Hamdioui, S. (author), Bertels, K.L.M. (author)
One of the most important constraints of today’s architectures for data-intensive applications is the limited bandwidth due to the memory-processor communication bottleneck. This significantly impacts performance and energy. For instance, the energy consumption share of communication and memory<br/>access may exceed 80%. Recently, the concept of...
conference paper 2016
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Ren, S. (author), Bertels, K.L.M. (author), Al-Ars, Z. (author)
In order to handle the massive raw data generated by next generation sequencing (NGS) platforms, GPUs are widely used by many genetic analysis tools to speed up the used algorithms. In this paper, we use GPUs to accelerate the pair-HMMs forward algorithm, which is used to calculate the overall alignment probability in many genomics analysis...
conference paper 2016
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Yu, J. (author), Nane, R. (author), Haron, M.A.B. (author), Hamdioui, S. (author), Corporaal, H (author), Bertels, K.L.M. (author)
Memristor-based Computation-in-Memory is one of the emerging architectures proposed to deal with Big Data problems. The design of such architectures requires a radically new automatic design flow because the memristor is a passive device that uses resistance to encode its logic value. This paper proposes a design flow for mapping parallel...
conference paper 2016
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Houtgast, E.J. (author), Sima, V.M. (author), Bertels, K.L.M. (author), Al-Ars, Z. (author)
We present the first accelerated implementation of BWA-MEM, a popular genome sequence alignment algorithm widely used in next generation sequencing genomics pipelines. The Smith-Waterman-like sequence alignment kernel requires a significant portion of overall execution time. We propose and evaluate a number of FPGA-based systolic array...
conference paper 2015
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Shahbahrami, A. (author), Pham, T.A. (author), Bertels, K.L.M. (author)
Texture features extraction algorithms are key functions in various image processing applications such as medical images, remote sensing, and content-based image retrieval. The most common way to extract texture features is the use of Gray Level Co-occurrence Matrices (GLCMs). The GLCM contains the second-order statistical information of spatial...
journal article 2011
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